Nanoindentation

LAMMPS input script

# Nanoindentation Example, Work in Progress

# ENH ericnhahn@gmail.com

# updated 2/20/2021

# !!!WORK IN PROGRESS!!!

# This input script is still in its testing phase, may be incomplete, inaccurate, include redundant pieces of code, etc.

# Collision of spherical penetrator on Silicon film

units metal

dimension 3

boundary p p f

atom_style atomic

neighbor 0.3 bin

neigh_modify every 1 delay 2 check yes

#VARIABLES

variable alattice equal 5.43

variable 1x1 equal 1

variable 1x2 equal 0

variable 1x3 equal 0

variable 1y1 equal 0

variable 1y2 equal 1

variable 1y3 equal 0

variable 1z1 equal 0

variable 1z2 equal 0

variable 1z3 equal 1

variable xsize1 equal "sqrt(v_1x1^2 + v_1x2^2 + v_1x3^2)"

variable ysize1 equal "sqrt(v_1y1^2 + v_1y2^2 + v_1y3^2)"

variable zsize1 equal "sqrt(v_1z1^2 + v_1z2^2 + v_1z3^2)"

#Target and projectile size, etc,

variable b equal 65 #a bit more than half allowing for bottom layers

variable bulk equal "round(v_b/v_zsize1)" #a bit more than half allowing for bottom layers

variable t equal 35

variable top equal "round(v_t/v_zsize1)"

variable xl equal 95

variable yl equal 95

variable xmin equal 0

variable x2 equal "round(v_xl/(2*v_xsize1))"

variable cx2 equal "v_x2+1"

variable xh equal "v_xl/2"

variable ymin equal 0

variable yh equal "v_yl/2"

variable y2 equal "round(v_yl/(2*v_ysize1))"

variable cy2 equal "v_y2+1"

variable radius equal 100

variable offset equal 10

variable center equal "v_radius+v_offset"

variable vdown equal -0.20 # 10 A/ps -> 1 km/s; 1=100 m/s; 0.1 = 10 m/s

variable vup equal "v_vdown*-2"

variable rundown equal 110000 # distance will equal vdown*ts*rundown

variable runhold equal 5000 # real value

variable runtemp equal 20000

variable runup equal "v_rundown*0.50"

variable ts equal 0.005

variable lowT equal 300

variable highT equal 800

variable tS equal 0.001

variable tdamp equal "v_tS*100"

variable pdamp equal "v_tS*1000"

variable tdump equal 500

variable fbulk equal "v_bulk-1"

variable tbulk equal "v_bulk-2"

variable txmin equal "v_xmin+1"

variable tx2 equal "v_x2-1"

variable tymin equal "v_ymin+1"

variable ty2 equal "v_y2-1"

# CREATE GEOMETRY

lattice diamond ${alattice} orient x ${1x1} ${1x2} ${1x3} orient y ${1y1} ${1y2} ${1y3} orient z ${1z1} ${1z2} ${1z3} spacing ${xsize1} ${ysize1} ${zsize1}

#lattice diamond ${alattice} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1

region box block -${x2} ${x2} -${y2} ${y2} -${bulk} ${top} units lattice

create_box 1 box

mass 1 28.08

#Create Atoms

region target block -${cx2} ${cx2} -${cy2} ${cy2} -${bulk} 0.0 units lattice

create_atoms 1 region target

group target region target

#POTENTIALS

pair_style tersoff/mod

pair_coeff * * Si.tersoff.mod Si

#pair_style tersoff

#pair_coeff * * SiCGe.tersoff Si(C) Si(C)

#pair_style sw

#pair_coeff * * Si.sw Si

# Regions

region inner block -${tx2} ${tx2} -${ty2} ${ty2} -${tbulk} INF units lattice

group inner region inner

region bottom block -${x2} ${x2} -${y2} ${y2} -${bulk} -${fbulk} units lattice

group bottom region bottom

region thermalize intersect 2 box inner side out

group thermalize region thermalize

#Integrator + compute

fix 1 all nvt temp ${highT} ${highT} 1.0

compute 1 target ke/atom

compute 2 target pe/atom

compute 3 target coord/atom 3.0

compute 4 target stress/atom pair

compute new3d inner temp #needed?

#THERMO

thermo 5

thermo_style custom step temp pe ke etotal press vol pxx pyy pzz pxy pxz pyz

thermo_modify temp new3d norm yes #check

# Minimization with CG

#minimize 1e-6 1e-8 1000 10000 #Not edited

#VELOCITIES

velocity target create ${lowT} 234234 temp new3d

#THERMALIZE

fix 2 inner temp/rescale 1 ${lowT} ${highT} 1.0 1.0 #edited

fix 3 thermalize langevin ${highT} ${highT} 1.0 699483 #edited

fix 4 bottom setforce 0.0 0.0 0.0 #ok

velocity bottom set 0.0000 0.0000 0.0000 #ok

# equilibration for 2000 steps

dump viz all custom ${tdump} dump.NI100_10nm_eqilMOD_${highT}K.* x y z vx vy vz type id c_1 c_2 c_3 c_4[1] c_4[2] c_4[3] c_4[4] c_4[5] c_4[6]

run ${runtemp} #run 1000

undump viz

# BEGIN NANOINDENTATION

reset_timestep 0

unfix 1

unfix 2

fix 1 all nve

variable z1 equal "vdisplace(v_center,v_vdown)"

# position above the surface, y velocity in angstroms/ps

fix 5 all indent 10.0 sphere 0 0 v_z1 v_radius units box

# Dump defects

#dump defects target custom ${tdump} dump.NI_def_SW_${highT}K.* x y z vx vy vz type id c_1 c_2 c_3 c_4[1] c_4[2] c_4[3]

#dump_modify defects thresh c_3 != 4 #edited for non dc

# dump for all atoms

dump 1 all custom 250 dump.NI10nm_All100_MOD_${highT}K.* x y z vx vy vz type id c_1 c_2 c_3 c_4[1] c_4[2] c_4[3] c_4[4] c_4[5] c_4[6]

thermo 10

thermo_style custom step temp pe ke etotal press vol pxx pyy pzz pxy pxz pyz f_5 f_5[1] f_5[2] f_5[3]

thermo_modify temp new3d norm yes #check

# === Gather and Print Indent Outputs and other useful plottables === #still need to add dumps for the displacement but for now can be calculated manually

run 0

variable timer equal "step"

variable temper equal "temp"

variable track equal "f_5"

variable track1 equal "f_5[1]" # X

variable track2 equal "f_5[2]" # Y

variable track3 equal "f_5[3]" # Z Indenter Force!

print "${timer} ${temper} ${track} ${track1} ${track2} ${track3}" append NI_outputs.txt

timestep ${ts}

run ${rundown}

unfix 5

variable newcen equal "v_center+v_vdown*v_ts*v_rundown"

fix 5 all indent 10.0 sphere 0 0 v_newcen v_radius units box

run ${runhold}

unfix 5

variable z2 equal "vdisplace(v_newcen,v_vup)"

fix 5 all indent 10.0 sphere 0 0 v_z2 v_radius units box

run ${runup}

print "Job's done!"